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Abel Torres Espin is an assistant adjunct professor at the Brain and Spinal Injury Center (BASIC), Department of Neurosurgery, at the University of California, San Francisco (UCSF).

His current research focuses on the intersection between neurotrauma research and data science. He applies, explores and develops data science methods in traumatic injuries affecting the brain and the spinal cord to increase reproducibility, accelerate translation and augment evidence-based medical practice. These methods include machine learning and intelligence analytics, open science, data sharing, data infrastructures, data mining and data visualization, among others.

He uses the programming language R as a primary tool, and Python from time to time.

Publications

2021


Topological network analysis of patient similarity for precision management of

Torres-Espin A; Haefeli J; Ehsanian R; Torres D; Almeida CA; Huie JR; Chou A; Morozov D; Sanderson N; Dirlikov B; Suen CG; Nielson JL; Kyritsis N; Hemmerle DD; Talbott JF; Manley GT; Dhall SS; Whetstone WD; Bresnahan JC; Beattie MS; McKenna SL; Pan JZ; Ferguson AR Elife. 2021 Nov 16;10. pii: 68015. doi: 10.7554/eLife.68015.

Promoting FAIR Data Through Community-driven Agile Design: the Open Data Commons

Torres-Espin A; Almeida CA; Chou A; Huie JR; Chiu M; Vavrek R; Sacramento J; Orr MB; Gensel JC; Grethe JS; Martone ME; Fouad K; Ferguson AR Neuroinformatics. 2021 Aug 4. pii: 10.1007/s12021-021-09533-8. doi:

Mixture Model Framework for Traumatic Brain Injury Prognosis Using Heterogeneous

Kaplan AD; Cheng Q; Mohan KA; Nelson LD; Jain S; Levin H; Torres-Espin A; Chou A; Huie JR; Ferguson AR; Mccrea M; Giacino J; Sundaram S; Markowitz AJ; Manley GT IEEE J Biomed Health Inform. 2021 Jul 26;PP. doi: 10.1109/JBHI.2021.3099745.

Beyond the lesion site: minocycline augments inflammation and anxiety-like

Schmidt EKA; Raposo PJF; Torres-Espin A; Fenrich KK; Fouad K J Neuroinflammation. 2021 Jun 26;18(1):144. doi: 10.1186/s12974-021-02123-0.

Excavating FAIR Data: the Case of the Multicenter Animal Spinal Cord Injury Study

Almeida CA; Torres-Espin A; Huie JR; Sun D; Noble-Haeusslein LJ; Young W; Beattie MS; Bresnahan JC; Nielson JL; Ferguson AR Neuroinformatics. 2021 Mar 2. pii: 10.1007/s12021-021-09512-z. doi:

Automation of training and testing motor and related tasks in pre-clinical

Mah KM; Torres-Espin A; Hallworth BW; Bixby JL; Lemmon VP; Fouad K; Fenrich KK Exp Neurol. 2021 Jun;340:113647. doi: 10.1016/j.expneurol.2021.113647. Epub 2021

Diagnostic blood RNA profiles for human acute spinal cord injury.

Kyritsis N; Torres-Espin A; Schupp PG; Huie JR; Chou A; Duong-Fernandez X; Thomas LH; Tsolinas RE; Hemmerle DD; Pascual LU; Singh V; Pan JZ; Talbott JF; Whetstone WD; Burke JF; DiGiorgio AM; Weinstein PR; Manley GT; Dhall SS; Ferguson AR; Oldham MC; Bresnahan JC; Beattie MS J Exp Med. 2021 Mar 1;218(3). pii: 211739. doi: 10.1084/jem.20201795.

Reproducible analysis of disease space via principal components using the novel R

Torres-Espin A; Chou A; Huie JR; Kyritsis N; Upadhyayula PS; Ferguson AR Elife. 2021 Jan 14;10. pii: 61812. doi: 10.7554/eLife.61812.

Self-directed rehabilitation training intensity thresholds for efficient recovery

Fenrich KK; Hallworth BW; Vavrek R; Raposo PJF; Misiaszek JE; Bennett DJ; Fouad K; Torres-Espin A Exp Neurol. 2021 May;339:113543. doi: 10.1016/j.expneurol.2020.113543. Epub 2020

Cisplatin-induced peripheral neuropathy is associated with neuronal

Calls A; Torres-Espin A; Navarro X; Yuste VJ; Udina E; Bruna J Neuro Oncol. 2021 Jan 30;23(1):88-99. doi: 10.1093/neuonc/noaa151.

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2020


Injury volume extracted from MRI predicts neurologic outcome in acute spinal cord

Mummaneni N; Burke JF; DiGiorgio AM; Thomas LH; Duong-Fernandez X; Harris M; Pascual LU; Ferguson AR; Russell Huie J; Pan JZ; Hemmerle DD; Singh V; Torres-Espin A; Omondi C; Kyritsis N; Weinstein PR; Whetstone WD; Manley GT; Bresnahan JC; Beattie MS; Cohen-Adad J; Dhall SS; Talbott JF J Clin Neurosci. 2020 Dec;82(Pt B):231-236. doi: 10.1016/j.jocn.2020.11.003. Epub

Transforming Research and Clinical Knowledge in Spinal Cord Injury (TRACK-SCI):

Tsolinas RE; Burke JF; DiGiorgio AM; Thomas LH; Duong-Fernandez X; Harris MH; Yue JK; Winkler EA; Suen CG; Pascual LU; Ferguson AR; Huie JR; Pan JZ; Hemmerle DD; Singh V; Torres-Espin A; Omondi C; Kyritsis N; Haefeli J; Weinstein PR; de Almeida Neto CA; Kuo YH; Taggard D; Talbott JF; Whetstone WD; Manley GT; Bresnahan JC; Beattie MS; Dhall SS Neurosurg Focus. 2020 May 1;48(5):E6. doi: 10.3171/2020.2.FOCUS191030.

Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal

Schmidt EKA; Torres-Espin A; Raposo PJF; Madsen KL; Kigerl KA; Popovich PG; Fenrich KK; Fouad K PLoS One. 2020 Jan 15;15(1):e0226128. doi: 10.1371/journal.pone.0226128.

Single-session cortical electrical stimulation enhances the efficacy of

Batty NJ; Torres-Espin A; Vavrek R; Raposo P; Fouad K Exp Neurol. 2020 Feb;324:113136. doi: 10.1016/j.expneurol.2019.113136. Epub 2019

FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal

Fouad K; Bixby JL; Callahan A; Grethe JS; Jakeman LB; Lemmon VP; Magnuson DSK; Martone ME; Nielson JL; Schwab JM; Taylor-Burds C; Tetzlaff W; Torres-Espin A; Ferguson AR J Neurotrauma. 2020 Mar 15;37(6):831-838. doi: 10.1089/neu.2019.6674. Epub 2019

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2018


Rehabilitative Training in Animal Models of Spinal Cord Injury.

Torres-Espin A; Beaudry E; Fenrich K; Fouad K J Neurotrauma. 2018 Aug 15;35(16):1970-1985. doi: 10.1089/neu.2018.5906.

Eliciting inflammation enables successful rehabilitative training in chronic

Torres-Espin A; Forero J; Fenrich KK; Lucas-Osma AM; Krajacic A; Schmidt E; Vavrek R; Raposo P; Bennett DJ; Popovich PG; Fouad K Brain. 2018 Jul 1;141(7):1946-1962. doi: 10.1093/brain/awy128.

A motorized pellet dispenser to deliver high intensity training of the single

Torres-Espin A; Forero J; Schmidt EKA; Fouad K; Fenrich KK Behav Brain Res. 2018 Jan 15;336:67-76. doi: 10.1016/j.bbr.2017.08.033. Epub 2017

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2017


Following Spinal Cord Injury Transected Reticulospinal Tract Axons Develop New

May Z; Fenrich KK; Dahlby J; Batty NJ; Torres-Espin A; Fouad K Neural Plast. 2017;2017:1932875. doi: 10.1155/2017/1932875. Epub 2017 Sep 12.

Cyclosporine-immunosuppression does not affect survival of transplanted

May Z; Torres-Espin A; Lucas-Osma AM; Batty NJ; Raposo P; Fenrich KK; Stykel MG; Fuhrmann T; Shoichet M; Biernaskie J; Fouad K Neurosci Lett. 2017 Sep 29;658:67-72. doi: 10.1016/j.neulet.2017.08.045. Epub

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2016


Effects of the Post-Spinal Cord Injury Microenvironment on the Differentiation

Lopez-Serrano C; Torres-Espin A; Hernandez J; Alvarez-Palomo AB; Requena J; Gasull X; Edel MJ; Navarro X Cell Transplant. 2016 Oct;25(10):1833-1852. doi: 10.3727/096368916X691312.

Beneficial effects of IL-37 after spinal cord injury in mice.

Coll-Miro M; Francos-Quijorna I; Santos-Nogueira E; Torres-Espin A; Bufler P; Dinarello CA; Lopez-Vales R Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1411-6. doi: 10.1073/pnas.1523212113.

Single pellet grasping following cervical spinal cord injury in adult rat using

Fenrich KK; May Z; Torres-Espin A; Forero J; Bennett DJ; Fouad K Behav Brain Res. 2016 Feb 15;299:59-71. doi: 10.1016/j.bbr.2015.11.020. Epub 2015

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2015


Increased migration of olfactory ensheathing cells secreting the Nogo receptor

Reginensi D; Carulla P; Nocentini S; Seira O; Serra-Picamal X; Torres-Espin A; Matamoros-Angles A; Gavin R; Moreno-Flores MT; Wandosell F; Samitier J; Trepat X; Navarro X; del Rio JA Cell Mol Life Sci. 2015 Jul;72(14):2719-37. doi: 10.1007/s00018-015-1869-3. Epub

Activity dependent therapies modulate the spinal changes that motoneurons suffer

Arbat-Plana A; Torres-Espin A; Navarro X; Udina E Exp Neurol. 2015 Jan;263:293-305. doi: 10.1016/j.expneurol.2014.10.009. Epub 2014

Immunosuppression of allogenic mesenchymal stem cells transplantation after

Torres-Espin A; Redondo-Castro E; Hernandez J; Navarro X J Neurotrauma. 2015 Mar 15;32(6):367-80. doi: 10.1089/neu.2014.3562. Epub 2015

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2014


Bone marrow mesenchymal stromal cells and olfactory ensheathing cells

Torres-Espin A; Redondo-Castro E; Hernandez J; Navarro X Eur J Neurosci. 2014 May;39(10):1704-17. doi: 10.1111/ejn.12542. Epub 2014 Mar

Dithiocarb (N,N-diethyldithiocarbamate, DEDTC) decreases levels of biogenic

Redondo-Castro E; Romero R; Torres-Espin A; Utrera J; Duque D; Junyent F; Auladell C Neuropathol Appl Neurobiol. 2014 Oct;40(6):747-58. doi: 10.1111/nan.12083.

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2013


Gene expression changes in the injured spinal cord following transplantation of

Torres-Espin A; Hernandez J; Navarro X PLoS One. 2013 Oct 11;8(10):e76141. doi: 10.1371/journal.pone.0076141.

Neuroprotection and axonal regeneration after lumbar ventral root avulsion by

Torres-Espin A; Corona-Quintanilla DL; Fores J; Allodi I; Gonzalez F; Udina E; Navarro X Neurotherapeutics. 2013 Apr;10(2):354-68. doi: 10.1007/s13311-013-0178-5.

Quantitative assessment of locomotion and interlimb coordination in rats after

Redondo-Castro E; Torres-Espin A; Garcia-Alias G; Navarro X J Neurosci Methods. 2013 Mar 15;213(2):165-78. doi:

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2011


Adult stem cell transplants for spinal cord injury repair: current state in

Hernandez J; Torres-Espin A; Navarro X Curr Stem Cell Res Ther. 2011 Sep;6(3):273-87. doi: 10.2174/157488811796575323.

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2010


Functional involvement of the lumbar spinal cord after contusion to T8 spinal

Garcia-Alias G; Torres-Espin A; Vallejo C; Navarro X No info

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Software

syndRomics: an R package for reproducible analysis of disease space via principal components

GitHub

Citation: Abel Torres-Espin, Austin Chou, J. Russell Huie, Nikos Kyritsis, Pavan Upadhyayula, and Adam R. Ferguson. Reproducible analysis of disease space via principal components using the novel R package syndRomics. https://doi.org/10.7554/eLife.61812


Neurite-J: an ImageJ plug in for axonal growth analysis in organotypic cultures

Download

Citation: Torres-Espín A, Santos D, González-Pérez F, del Valle J, Navarro X. Neurite-J: An Image-J plug-in for axonal analisys in organotypic cultures. J Neurosci Meth 236:26–39

About

Abel was born in Mataro, close to Barcelona, Spain. He studied biology at the Universitat de Barcelona from 2002 to 2007. In 2008 he started his PhD in the neuroscience program at the Universitat Autonoma de Barcelona under the supervision of Dr. Xavier Navarro, finishing his thesis entitled ‘Terapia celular para lesiones que afectan a la medula espinal’ (Cell therapy for injuries affecting the spinal cord). In 2014, Abel moved to Edmonton, Canada, for a postdoctoral position at the University of Alberta under the supervision of Dr. Karim Fouad. Here, he worked on the interaction between neuroinflammation and rehabilitative motor training after cervical spinal cord injury. Since November 2018, he have been working at the University of California San Francisco in a team led by Dr. Adam Ferguson, where they work on the application of data science to accelerate neurotrauma research and translation.

When Abel is not doing research or coding, he is visiting mountains, climbing or catching up with friends.

This website

This website has been created in R, using Rmarkdown and the flexdashboard package. It is an attempt to produce a light weight academic webpage. Other options such as blogdown are possible, and I recommend to explore them. After trying with several options, I decided using trying flexdashboard, which its primary use is for fast creation of dashboard in R. I found the multi-page layout and the incorporation of custom CSS code sufficient to produce this page. Some limitations of this light weight site is the difficulty to incorporate more dynamic content such as a blog.

Automatic publications: the publication section is is automatically populated every knitting by querying PubMed using the easyPubMed R package interfacing with PubMed API. You can see the source code using the navigation var (top right corner) or in GitHub.

This makes very easy to update the page by updating the Rmarkdown, knitting and pushing to GitHub.

---
title: "Abel Torres Espin"
output: 
  flexdashboard::flex_dashboard:
    theme:
      version: 4
    social: [ "menu" ]
    source_code: embed
    css: webFlex.css
    vertical_layout: fill
editor_options: 
  chunk_output_type: console
---

```{r setup, include=FALSE}
library(flexdashboard)
library(easyPubMed) #API connection with pubmed
library(tidyverse) #To facilitate some data wrangling
library(DT) # for table html formatting
library(htmltools)
```

Home
=====================================

:::{.intro .justify}

Abel Torres Espin is an assistant adjunct professor at the [Brain and Spinal Injury Center (BASIC)](https://brainandspinalinjury.org/), Department of Neurosurgery, at the University of California, San Francisco (UCSF). 

His current research focuses on the intersection between neurotrauma research and data science. He applies, explores and develops data science methods in traumatic injuries affecting the brain and the spinal cord to increase reproducibility, accelerate translation and augment evidence-based medical practice. These methods include machine learning and intelligence analytics, open science, data sharing, data infrastructures, data mining and data visualization, among others.

He uses the programming language R as a primary tool, and Python from time to time.
:::

:::{.footnote .justify}
Abel.torresespin@ucsf.edu || [GitHub](https://github.com/ATEspin) || [UCSF profile](https://profiles.ucsf.edu/abel.torresespin) || [Google Scholar](https://scholar.google.com/citations?user=c7vjfOUAAAAJ&hl=en)
:::

Publications
=====================================

```{r}
## This creates a search that gets saved in NML servers with specific ids, that makes the query reusable without the need to search again.
my_entrez_id <- get_pubmed_ids('Abel Torres-Espin')

## This fetches the pubmed info for each paper returned as list of string character vector
track_txt <- fetch_pubmed_data(my_entrez_id, format = "medline")

## Creates an index of where the papers start in the track_txt string
paper_list_index<-c(which(track_txt==""),length(track_txt))

## Extract papers by list
paper_list<-list()
for(i in 1:(length(paper_list_index)-1)){
  paper_list[[i]]<-track_txt[seq(paper_list_index[i],paper_list_index[i+1]-1)]
}

## List of PMIDs using the PMID tag
PMC_list<-track_txt[str_detect(track_txt, "^PMID- ")]
PMC_list<-unique(str_remove_all(PMC_list, '^PMID- '))

### build the dataframe
extract<-list()
for (p in 1:length(paper_list)){
  i<-paper_list[[p]]
  ## Author names
  author_names<-i[str_detect(i, "^AU ")]
  author_names<-paste0(str_remove_all(author_names, "^AU  - "), collapse="; ")
  
  ## PMIDs
  PMID<-i[str_detect(i, "^PMID- ")]
  PMID<-str_remove_all(PMID, '^PMID- ')
  
  ## Date publication
  date_p<-i[str_detect(i, "^DP ")]
  date_p<-str_remove_all(date_p, '^DP  - ')
  
  ## year
  year<-str_extract(date_p,"[[:digit:]]+")
  
  ## Title
  title<-i[str_detect(i, "^TI ")]
  title<-str_remove_all(title, '^TI  - ')
  
  ## Publication info
  pub_info<-i[str_detect(i, "^SO ")]
  pub_info<-str_remove_all(pub_info, '^SO  - ')
  
  ## DOI
  lid<-i[str_detect(i, "^LID ")]
  lid<-str_remove_all(lid, '^LID - ')
  
  if (length(lid)>0){
    if (str_detect(lid, "doi")){
      lid<-str_remove_all(lid, ' .+')
      lid<-paste0("https://doi.org/", lid)
    }else{
      lid<-NULL
    }
  }else{
    lid<-NULL
  }
  
  ## join all info in dataframe
  extract[[p]]<-data.frame("Year" = ifelse(is_empty(year), "No year", year),
                           "Title" = ifelse(is_empty(title), "No title", title), 
                           "Authors" = ifelse(is_empty(author_names), 
                                              "No names", author_names), 
                           "Info" = ifelse(is_empty(pub_info), "No info", pub_info), 
                           "PMID" = ifelse(is_empty(PMID), "No PMID", PMID),
                           "DOI" = ifelse(is_empty(lid), "No DOI", lid))
}

## Create the dataframe
pub_df<-do.call(rbind, extract)
pub_df<-pub_df%>%arrange(Year)
pub_df$Link<-paste0("https://pubmed.ncbi.nlm.nih.gov/", pub_df$PMID)
```

```{r }
# pub_df<-pub_df%>%select(-DOI)
# datatable(pub_df)

year_list<-list()
years<-sort(unique(pub_df$Year), decreasing = T)
for (i in 1:length(years)){
  year<-years[i]
  temp_df<-pub_df[pub_df$Year==year,]
  ## papers per year
  temp_tags<-apply(temp_df, 1, function(x){
              list(
                tags$h5(
                (if (!is.na(x[5])) {
                    tags$a(href = x[6],x[2])
                }else{
                    tags$a(x[2])
                })),
                tags$p(x[3],x[4])
              )
           })
  
  year_list[[i]]<-
    tags$div(class = year,
          tags$h4(year),
          tags$hr(),
          temp_tags,
          tags$a(href="#top","Back to top"),
          tags$br()
      )
}

x<-tags$div(class="top",
           year_list)

x

# write.table(htmltools::renderTags(x)$html, file = "test.txt", quote = F, row.names = F)
```

Software
=====================================

:::{.mainText .justify}
`syndRomics`: an R package for reproducible analysis of disease space via principal components



[GitHub](https://github.com/ucsf-ferguson-lab/syndRomics)

**Citation**: Abel Torres-Espin, Austin Chou, J. Russell Huie, Nikos Kyritsis, Pavan Upadhyayula, and Adam R. Ferguson. Reproducible analysis of disease space via principal components using the novel R package syndRomics. https://doi.org/10.7554/eLife.61812
:::
***
:::{.mainText .justify}
`Neurite-J`: an ImageJ plug in for axonal growth analysis in organotypic cultures



[Download](https://imagejdocu.tudor.lu/plugin/analysis/neurite-j/start)

**Citation**: Torres-Espín A, Santos D, González-Pérez F, del Valle J, Navarro X. Neurite-J: An Image-J plug-in for axonal analisys in organotypic cultures. J Neurosci Meth 236:26–39
:::

:::{.footnote .justify}
Abel.torresespin@ucsf.edu || [GitHub](https://github.com/ATEspin) || [UCSF profile](https://profiles.ucsf.edu/abel.torresespin) || [Google Scholar](https://scholar.google.com/citations?user=c7vjfOUAAAAJ&hl=en)
:::

About
=====================================

:::{.mainText .justify}

Abel was born in Mataro, close to Barcelona, Spain. He studied biology at the Universitat de Barcelona from 2002 to 2007. In 2008 he started his PhD in the neuroscience program at the Universitat Autonoma de Barcelona under the supervision of Dr. Xavier Navarro, finishing his thesis entitled ‘Terapia celular para lesiones que afectan a la medula espinal’ (Cell therapy for injuries affecting the spinal cord). In 2014, Abel moved to Edmonton, Canada, for a postdoctoral position at the University of Alberta under the supervision of Dr. Karim Fouad. Here, he worked on the interaction between neuroinflammation and rehabilitative motor training after cervical spinal cord injury. Since November 2018, he have been working at the University of California San Francisco in a team led by Dr. Adam Ferguson, where they work on the application of data science to accelerate neurotrauma research and translation.

When Abel is not doing research or coding, he is visiting mountains, climbing or catching up with friends.

:::

:::{.footnote .justify}
Abel.torresespin@ucsf.edu || [GitHub](https://github.com/ATEspin) || [UCSF profile](https://profiles.ucsf.edu/abel.torresespin) || [Google Scholar](https://scholar.google.com/citations?user=c7vjfOUAAAAJ&hl=en)
:::

This website
=====================================

:::{.mainText .justify}

This website has been created in R, using Rmarkdown and the [flexdashboard](https://pkgs.rstudio.com/flexdashboard/) package. It is an attempt to produce a light weight academic webpage. Other options such as [blogdown](https://bookdown.org/yihui/blogdown/) are possible, and I recommend to explore them. After trying with several options, I decided using trying flexdashboard, which its primary use is for fast creation of dashboard in R. I found the multi-page layout and the incorporation of custom CSS code sufficient to produce this page. Some limitations of this light weight site is the difficulty to incorporate more dynamic content such as a blog.

**Automatic publications**: the publication section is is automatically populated every knitting by querying PubMed using the [easyPubMed](https://cran.r-project.org/web/packages/easyPubMed/index.html) R package interfacing with PubMed API. You can see the source code using the navigation var (top right corner) or in [GitHub](https://github.com/ATEspin/ATEspin.github.io).

This makes very easy to update the page by updating the Rmarkdown, knitting and pushing to GitHub.

:::

:::{.footnote .justify}
Abel.torresespin@ucsf.edu || [GitHub](https://github.com/ATEspin) || [UCSF profile](https://profiles.ucsf.edu/abel.torresespin) || [Google Scholar](https://scholar.google.com/citations?user=c7vjfOUAAAAJ&hl=en)
:::